City investigators seized boxes of documents and computer files from Chicago’s Commission on Animal Care and Control on Thursday — and took pictures of conditions at the city pound — amid allegations that a dog was mistakenly euthanized and that employees may have tried to cover up their mistake.

Inspector General David Hoffman said he ordered the raid at 2741 S. Western, but he would not reveal the nature of his internal investigation.

In recent weeks, investigators have been asking at the pound about a mistakenly killed dog, controlled substances used to euthanize animals and about missing documents related to the incident, City Hall sources said.

‘You tell the truth’

The investigation into what the sources described as a “potential cover-up” culminated in Thursday’s raid. Investigators arrived at Animal Care with cameras, took pictures of conditions at the facility and left with boxes of documents and computer files. It was not known whether the raid was related to the earlier interviews of Animal Care employees.

“I can confirm that inspector general investigators took records from the Animal Care and Control facility [Thursday]. This is part of an ongoing investigation,” said Hoffman, the former federal prosecutor hired to root out City Hall corruption in the wake of the Hired Truck, city hiring and minority contracting scandals. “We received the complete cooperation from the commissioner.”

Anne Kent, executive director of the Commission on Animal Care and Control, did not return repeated phone calls.

Dr. Gene Mueller, the former executive director of Animal Care and Control now serving as president of the Anti-Cruelty Society, was taken aback by the cover-up charge.

“Misidentification of a dog can certainly happen when you’re dealing with large numbers of animals. But if it happens, you tell the truth. Being forthright is the way to deal with it,” Mueller said.

Ald. Eugene Schulter (47th), who spearheaded a rewrite of the city’s animal care ordinance, called the cover-up allegations “absolutely astonishing.” He said the City Council would conduct its own investigation.

“We’re supposed to be caring for animals and treating them humanely,” said Schulter, who chairs the City Council’s License Committee.

‘Inundated with animals’

In January 2005, Kent’s predecessor, Nikki Proutsos, resigned her $87,756-a-year job amid allegations that dogs at the city pound were lying in their own waste and power-washed while inside their cages. The allegations came from volunteers who donate their time at 2741 S. Western.

At the time, Proutsos said she was aware of the complaints, but denied that dogs had been mistreated. She was reassigned to oversee nutrition programs for the city’s Department of Aging.